Adding a new Header tha fakes the original one but using the netCDF4 …

…file

reflexible/__init__.py

@@ -103,3 +103,4 @@ def print_versions():
 from .tests.all import test
 from . import conv2netcdf4
 from .scripts.create_ncfile import create_ncfile
+from .data_structures import Header

reflexible/data_structures.py

@@ -0,0 +1,299 @@
+"""
+Definition of the different data structures in reflexible.
+"""
+
+import datetime
+
+import numpy as np
+import netCDF4 as nc
+
+
+class Header(object):
+    """This is the primary starting point for processing FLEXPART output.
+
+    It contains all the metadata from the simulation run and tries to
+    fake the behaviour of the `Header` of former ``pflexible`` package
+    (that still lives in the ``reflexible.conv2netcdf4`` subpackage).
+
+    This version is using a netCDF4 file instead of a native FLEXPART
+    format.
+
+    Usage::
+
+        > H = Header(inputpath)
+        > dir(H)   # provides a list of available attributes
+
+    Parameters
+    -----------
+      path : string
+        The path of the netCDF4 file.
+
+    """
+
+    @property
+    def outlon0(self):
+        return self.nc.outlon0
+
+    @property
+    def outlat0(self):
+        return self.nc.outlat0
+
+    @property
+    def dxout(self):
+        return self.nc.dxout
+
+    @property
+    def dyout(self):
+        return self.nc.dyout
+
+    @property
+    def ibdate(self):
+        return self.nc.ibdate
+
+    @property
+    def ibtime(self):
+        return self.nc.ibtime
+
+    @property
+    def iedate(self):
+        return self.nc.iedate
+
+    @property
+    def ietime(self):
+        return self.nc.ietime
+
+    @property
+    def loutstep(self):
+        return self.nc.loutstep
+
+    @property
+    def loutaver(self):
+        return self.nc.loutaver
+
+    @property
+    def loutsample(self):
+        return self.nc.loutsample
+
+    @property
+    def loutsample(self):
+        return self.nc.loutsample
+
+    @property
+    def lsubgrid(self):
+        return self.nc.lsubgrid
+
+    @property
+    def lconvection(self):
+        return self.nc.lconvection
+
+    @property
+    def ind_source(self):
+        return self.nc.ind_source
+
+    @property
+    def ind_receptor(self):
+        return self.nc.ind_receptor
+
+    @property
+    def ldirect(self):
+        return self.nc.ldirect
+
+    @property
+    def direction(self):
+        if self.nc.ldirect < 0:
+            return "backward"
+        else:
+            return "forward"
+    @property
+    def numxgrid(self):
+        return len(self.nc.dimensions['longitude'])
+
+    @property
+    def numygrid(self):
+        return len(self.nc.dimensions['latitude'])
+
+    @property
+    def longitude(self):
+        return np.arange(self.outlon0,
+                         self.outlon0 + (self.dxout * self.numxgrid),
+                         self.dxout)
+
+    @property
+    def latitude(self):
+        return np.arange(self.outlat0,
+                         self.outlat0 + (self.dyout * self.numygrid),
+                         self.dyout)
+
+    @property
+    def available_dates(self):
+        loutstep = self.nc.loutstep
+        nsteps = len(self.nc.dimensions['time'])
+        d = datetime.datetime.strptime(self.nc.iedate + self.nc.ietime,
+                                       "%Y%m%d%H%M%S")
+        l = [(d + datetime.timedelta(seconds=t)).strftime("%Y%m%d%H%M%S")
+            for t in range(loutstep * (nsteps - 1),
+                           -loutstep, -loutstep)]
+        return l
+
+    @property
+    def ireleasestart(self):
+        return self.nc.variables['RELSTART']
+
+    @property
+    def ireleaseend(self):
+        return self.nc.variables['RELEND']
+
+    @property
+    def releasestart(self):
+        rel_start = self.nc.variables['RELSTART'][::-1]
+        d = datetime.datetime.strptime(self.nc.iedate + self.nc.ietime,
+                                       "%Y%m%d%H%M%S")
+        return [(d - datetime.timedelta(seconds=int(t))) for t in rel_start]
+
+    @property
+    def releaseend(self):
+        rel_end = (self.nc.variables['RELEND'][::-1] +
+                   self.nc.variables['RELSTART'][-1] * 2)  # XXX ugly workaround
+        d = datetime.datetime.strptime(self.nc.iedate + self.nc.ietime,
+                                       "%Y%m%d%H%M%S")
+        return [(d - datetime.timedelta(seconds=int(t))) for t in rel_end]
+
+    @property
+    def releasetimes(self):
+        return [b - ((b - a) / 2)
+                for a, b in zip(self.releasestart, self.releaseend)]
+
+    def __init__(self, path=None):
+        self.nc = nc.Dataset(path, 'r')
+
+    def __getitem__(self, key):
+        return getattr(self, key)
+
+    def keys(self):
+        not_listed = ["keys", "fill_backward", "add_trajectory"]
+        return [k for k in dir(self)
+                if not k.startswith('_') and k not in not_listed]
+
+    def _read_grid(self, **kwargs):
+        """ see :func:`read_grid` """
+        self.FD = FD = FDC()
+        self.FD = reflexible.conv2netcdf4.read_grid(self, **kwargs)
+
+    def fill_backward(self, **kwargs):
+        """ see :func:`fill_backward` """
+        reflexible.conv2netcdf4.fill_grids(self, **kwargs)
+
+    def add_trajectory(self):
+        """ see :func:`read_trajectories` """
+        self.trajectory = reflexible.conv2netcdf4.read_trajectories(self)
+
+
+class FDC(object):
+    """ Brief explanation of what represents this class.
+    """
+    def __init__(self):
+        self._keys = [
+            'grid', 'gridfile', 'itime', 'timestamp', 'species', 'rel_i',
+            'spec_i', 'dry', 'wet', 'slabs', 'shape', 'max', 'min']
+        for key in self._keys:
+            setattr(self, "_" + key, None)
+
+    def keys(self):
+        return self._keys
+
+    @property
+    def grid(self):
+        return self._grid
+
+    @grid.setter
+    def grid(self, value):
+        self._grid = value
+        self._shape = value.shape
+        self._max = value.max()
+        self._min = value.min()
+
+    @property
+    def gridfile(self):
+        return self._gridfile
+
+    @gridfile.setter
+    def gridfile(self, value):
+        self._gridfile = value
+
+    @property
+    def itime(self):
+        return self._itime
+
+    @itime.setter
+    def itime(self, value):
+        self._itime = value
+
+    @property
+    def timestamp(self):
+        return self._timestamp
+
+    @timestamp.setter
+    def timestamp(self, value):
+        self._timestamp = value
+
+    @property
+    def species(self):
+        return self._species
+
+    @species.setter
+    def species(self, value):
+        self._species = value
+
+    @property
+    def rel_i(self):
+        return self._rel_i
+
+    @rel_i.setter
+    def rel_i(self, value):
+        self._rel_i = value
+
+    @property
+    def spec_i(self):
+        return self._spec_i
+
+    @spec_i.setter
+    def spec_i(self, value):
+        self._spec_i = value
+
+    @property
+    def wet(self):
+        """I'm the 'wet' property."""
+        return self._wet
+
+    @wet.setter
+    def wet(self, value):
+        self._wet = value
+
+    @property
+    def dry(self):
+        return self._dry
+
+    @dry.setter
+    def dry(self, value):
+        self._dry = value
+
+    @property
+    def slabs(self):
+        return self._slabs
+
+    @slabs.setter
+    def slabs(self, value):
+        self._slabs = value
+
+    # Read-only properties
+    @property
+    def shape(self):
+        return self._shape
+
+    @property
+    def max(self):
+        return self._max
+
+    @property
+    def min(self):
+        return self._min